Microbiological profile of pathogens causing periprosthetic joint infection (PJI) after primary total hip (THA) and knee (TKA) arthroplasty varies in different regions, clinics and even departments. The objective of this study was to analyze the pathogen structure in patients with PJI after primary THA and TKA and its influence on the effectiveness of the infection eradication after two-stage reimplantation. We collected the retrospective data of 364 patients-161 with PJI after primary TKA (113 treated in two stages 48 with failure after spacer implantation) and 203 patients with infected THA (127 after successful two-stage reimplantation and 76 with PJI recurrence after the first stage) within the time period from January 2012 to December 2017, treated with two-stage protocol in the single center. A comparative analysis of pathogen structure was performed between cohorts of patients with hip and knee PJI. A subanalysis was made between the subsets comprised from patients with successful two-stage treatment and the subsets with failure to treat the infection. Staphylococcus epidermidis was the most commonly identified pathogen in the full hip and knee cohorts: 30.1% and 32.5%, respectively. However, the percentage of methicillin-resistant Staphylococcus epidermidis (MRSE) among all S. epidermidis isolates was higher in the hip cohort-50% compared with 35% in the knee cohort (p = 0.073). Other coagulase-negative Staphylococci were more common to patients with PJI after primary TKA-10.3% compared with 5% (p < 0.02). Streptococcus sp. caused hip PJI in a larger percentage of cases than in knee PJI (p < 0.01)-7% and 2%, respectively (p < 0.01). Polymicrobial associations were significantly more common in hip PJI compared to knee PJI: 45.3% and 14% of cases, respectively (p < 0.001). The presence of polymicrobial infection significantly raised the risk of PJI recurrence [OR 2 (95% CI from 1.24 to 3.24)] in knee PJI patients and reduced the effectiveness of infection eradication from 73.9% to 47.8%. Comparative analysis showed significant differences in the structure of PJI pathogens in the hip and knee. These findings are useful when choosing treatment strategies and empirical antibiotics regimens, in the management of patients with PJIs after primary hip and knee arthroplasty.